{
  "_id": "6a1e955b1d7bb097a0a6b9ed",
  "Package": "randRotation",
  "Title": "Random Rotation Methods for High Dimensional Data with Batch\nStructure",
  "Version": "1.25.0",
  "Authors@R": "person(given = \"Peter\",\nfamily = \"Hettegger\",\nrole = c(\"aut\", \"cre\"),\nemail = \"p.hettegger@gmail.com\",\ncomment = c(ORCID = \"0000-0001-8557-588X\"))",
  "Description": "A collection of methods for performing random rotations on\nhigh-dimensional, normally distributed data (e.g. microarray or\nRNA-seq data) with batch structure. The random rotation\napproach allows exact testing of dependent test statistics with\nlinear models following arbitrary batch effect correction\nmethods.",
  "License": "GPL-3",
  "biocViews": "Software, Sequencing, BatchEffect, BiomedicalInformatics,\nRNASeq, Preprocessing, Microarray, DifferentialExpression,\nGeneExpression, Genetics, MicroRNAArray, Normalization,\nStatisticalMethod",
  "Encoding": "UTF-8",
  "RdMacros": "Rdpack",
  "RoxygenNote": "7.2.3",
  "VignetteBuilder": "knitr",
  "URL": "https://github.com/phettegger/randRotation",
  "BugReports": "https://github.com/phettegger/randRotation/issues",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:52:30 UTC",
  "RemoteUrl": "https://github.com/bioc/randRotation",
  "RemoteRef": "HEAD",
  "RemoteSha": "6f4dc85f9f8320e82c3f36757a2826533d43b4cb",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-02 08:27:50 UTC",
    "User": "root"
  },
  "Author": "Peter Hettegger [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-8557-588X>)",
  "Maintainer": "Peter Hettegger <p.hettegger@gmail.com>",
  "MD5sum": "8f73ca4e01bfa1c79b43814a987a0dde",
  "_user": "bioc",
  "_type": "src",
  "_file": "randRotation_1.25.0.tar.gz",
  "_fileid": "baf2b54930f8fee841f719b8dfe967edc3452e239049f8f55698b2fc205d8b27",
  "_filesize": 1518318,
  "_sha256": "baf2b54930f8fee841f719b8dfe967edc3452e239049f8f55698b2fc205d8b27",
  "_created": "2026-06-02T08:27:50.000Z",
  "_published": "2026-06-02T08:33:31.680Z",
  "_jobs": [
    {
      "job": 79030218829,
      "time": 140,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7352736500"
    },
    {
      "job": 79030218885,
      "time": 166,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "7352745782"
    },
    {
      "job": 79030218839,
      "time": 299,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7352791796"
    },
    {
      "job": 79030218803,
      "time": 105,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "7352732918"
    },
    {
      "job": 79030218940,
      "time": 127,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7352750494"
    },
    {
      "job": 79029397307,
      "time": 298,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7352689049"
    },
    {
      "job": 79030218818,
      "time": 135,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7352734253"
    },
    {
      "job": 79030218878,
      "time": 131,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "7352733073"
    },
    {
      "job": 79030218955,
      "time": 123,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7352730953"
    },
    {
      "job": 79030219021,
      "time": 124,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7352731067"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 2,
    "note": 10
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26807703485",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/randRotation",
  "_commit": {
    "id": "6f4dc85f9f8320e82c3f36757a2826533d43b4cb",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777380750
  },
  "_maintainer": {
    "name": "Peter Hettegger",
    "email": "p.hettegger@gmail.com",
    "login": "phettegger",
    "description": "",
    "uuid": 22321986,
    "orcid": "0000-0001-8557-588X"
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "Rdpack",
      "version": ">= 0.7",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "BiocParallel",
      "role": "Suggests"
    },
    {
      "package": "lme4",
      "role": "Suggests"
    },
    {
      "package": "nlme",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 2.1.0",
      "role": "Suggests"
    },
    {
      "package": "limma",
      "role": "Suggests"
    },
    {
      "package": "sva",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.25.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.23.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "software",
    "sequencing",
    "batcheffect",
    "biomedicalinformatics",
    "rnaseq",
    "preprocessing",
    "microarray",
    "differentialexpression",
    "geneexpression",
    "genetics",
    "micrornaarray",
    "normalization",
    "statisticalmethod"
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "phettegger",
      "count": 50,
      "uuid": 22321986
    },
    {
      "user": "nturaga",
      "count": 10,
      "uuid": 2746443
    },
    {
      "user": "jwokaty",
      "count": 2,
      "uuid": 1744257
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 294,
    "source": "https://www.bioconductor.org/packages/stats/bioc/randRotation"
  },
  "_devurl": "https://github.com/phettegger/randrotation",
  "_searchresults": 5,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/randRotation.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/phettegger/randrotation",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "contrastModel",
    "initBatchRandrot",
    "initRandrot",
    "pFdr",
    "qqunif",
    "randorth",
    "randpermut",
    "randrot",
    "rotateStat",
    "show",
    "weights",
    "X_decomp"
  ],
  "_help": [
    {
      "page": "randRotation-package",
      "title": "randRotation: Random Rotation Methods for High Dimensional Data with Batch Structure",
      "topics": [
        "randRotation-package",
        "randRotation"
      ]
    },
    {
      "page": "contrastModel",
      "title": "Create transformed model matrix for contrast rotation",
      "topics": [
        "contrastModel"
      ]
    },
    {
      "page": "dim",
      "title": "Dimensions of an Object",
      "topics": [
        "dim,initBatchRandrot-method",
        "dim,initRandrot-method"
      ]
    },
    {
      "page": "dimnames",
      "title": "Dimnames of an Object",
      "topics": [
        "dimnames,initBatchRandrot-method",
        "dimnames,initRandrot-method"
      ]
    },
    {
      "page": "initBatchRandrot-class",
      "title": "Initialised random rotation batch object",
      "topics": [
        "initBatchRandrot-class"
      ]
    },
    {
      "page": "initRandrot",
      "title": "Initialisation of a random rotation Object",
      "topics": [
        "initBatchRandrot",
        "initBatchRandrot,list-method",
        "initRandrot",
        "initRandrot,list-method"
      ]
    },
    {
      "page": "initRandrot-class",
      "title": "Initialised random rotation class",
      "topics": [
        "initRandrot-class",
        "initRandrotW-class"
      ]
    },
    {
      "page": "pFdr",
      "title": "Calculate resampling based p-values and FDRs",
      "topics": [
        "pFdr"
      ]
    },
    {
      "page": "qqunif",
      "title": "Quantile-Quantile plot of data sample against uniform theoretical quantiles",
      "topics": [
        "qqunif"
      ]
    },
    {
      "page": "randorth",
      "title": "Random orthogonal matrix",
      "topics": [
        "randorth"
      ]
    },
    {
      "page": "randpermut",
      "title": "Generate random permutation matrix for n samples",
      "topics": [
        "randpermut"
      ]
    },
    {
      "page": "randrot",
      "title": "Random rotation of initialised object",
      "topics": [
        "randrot",
        "randrot,initBatchRandrot-method",
        "randrot,initRandrot-method",
        "randrot,initRandrotW-method"
      ]
    },
    {
      "page": "randRotation-defunct",
      "title": "Defunct functions in package 'randRotation'",
      "topics": [
        "df_estimate"
      ]
    },
    {
      "page": "rotateStat",
      "title": "Generate data rotations and calculate statistics on it",
      "topics": [
        "rotateStat"
      ]
    },
    {
      "page": "rotateStat-class",
      "title": "Rotated object containing rotated and non-rotated statistics",
      "topics": [
        "rotateStat-class"
      ]
    },
    {
      "page": "show",
      "title": "Show an Object",
      "topics": [
        "show,initBatchRandrot-method",
        "show,initRandrot-method",
        "show,rotateStat-method"
      ]
    },
    {
      "page": "weights",
      "title": "Extract model weights",
      "topics": [
        "weights,initBatchRandrot-method",
        "weights,initRandrot-method"
      ]
    },
    {
      "page": "X_decomp",
      "title": "Decomposition of the design matrix for random rotation generation",
      "topics": [
        "X_decomp"
      ]
    }
  ],
  "_rundeps": [
    "rbibutils",
    "Rdpack"
  ],
  "_vignettes": [
    {
      "source": "randRotationIntro.Rmd",
      "filename": "randRotationIntro.html",
      "title": "Random Rotation Package Introduction",
      "author": "Peter Hettegger",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installation",
        "Sample dataset",
        "Quick start - linear models with batch effect correction",
        "Basic principle of random rotation methods",
        "Batch effect correction with subsequent linear model analysis",
        "Skewed null distribution of p values",
        "Unskewed p-values by random rotation",
        "Resampling based FDR",
        "Contrasts",
        "How many rotations ?",
        "Correlation matrices with non-block design",
        "Batch effect correction with linear mixed models",
        "Sample dataset",
        "Estimation of cormat",
        "Random rotation",
        "Session info",
        "References"
      ],
      "created": "2020-01-03 11:20:22",
      "modified": "2021-02-09 09:12:13",
      "commits": 20
    }
  ],
  "_score": 3.6020599913279625,
  "_indexed": true,
  "_nocasepkg": "randrotation",
  "_universes": [
    "bioc",
    "phettegger"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.25.0",
      "date": "2026-06-02T08:30:27.000Z",
      "distro": "noble",
      "commit": "6f4dc85f9f8320e82c3f36757a2826533d43b4cb",
      "fileid": "cd50f909900b5f409ee19feaacfe721cecf40a6b6f8bc54d0cca44312f92d1e5",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26807703485"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.25.0",
      "date": "2026-06-02T08:32:36.000Z",
      "distro": "noble",
      "commit": "6f4dc85f9f8320e82c3f36757a2826533d43b4cb",
      "fileid": "3e81c9389d464f5b2496cd7e9a219865457147470591875cbb01c75fbaab286e",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26807703485"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.25.0",
      "date": "2026-06-02T08:30:00.000Z",
      "commit": "6f4dc85f9f8320e82c3f36757a2826533d43b4cb",
      "fileid": "37981c4c65fce93b343de5934e39c2f97d833fb51a349e25c15b66f7643547e3",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26807703485"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.25.0",
      "date": "2026-06-02T08:30:47.000Z",
      "commit": "6f4dc85f9f8320e82c3f36757a2826533d43b4cb",
      "fileid": "670a554427f0f4dd18ae011ce4a7e942cf8f1f2baaf13ad5a117ead205ee8d73",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26807703485"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.25.0",
      "date": "2026-06-02T08:30:26.000Z",
      "commit": "6f4dc85f9f8320e82c3f36757a2826533d43b4cb",
      "fileid": "6e9e38c45644bb4c5e3dd1ed7c8676ffc866cc6311c8172b64bb1db1d129eb45",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26807703485"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.25.0",
      "date": "2026-06-02T08:29:41.000Z",
      "commit": "6f4dc85f9f8320e82c3f36757a2826533d43b4cb",
      "fileid": "0c09e9c65d01190890fa3fae501d7beee08523ef6983b2738f0bf01d69cdee60",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26807703485"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.25.0",
      "date": "2026-06-02T08:29:31.000Z",
      "commit": "6f4dc85f9f8320e82c3f36757a2826533d43b4cb",
      "fileid": "5e441fdeb4034a48a9817f83d325babe6772883b3b638be47cf23299c34b7167",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26807703485"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.25.0",
      "date": "2026-06-02T08:29:36.000Z",
      "commit": "6f4dc85f9f8320e82c3f36757a2826533d43b4cb",
      "fileid": "2bfb048aada4ce7aa0df9cb7b4287cf86228539bc08bd040a4fecfb95fd8bd58",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26807703485"
    }
  ]
}